Genetic Maps

Description

Around 1,000 known genetic markers exist for Neurospora crassa.
Some of these markers have been ordered on seven linkage group genetic
maps. The genetic map information was kindly provided by Alan Radford,
David Perkins and Matt Sachs. See the 1982
Compendium FGSC genetic maps for more details, or visit the updated
2000
version. Additional genetic map data was compiled by Roll Jean
Cheng and Alex Harry as part of the Apprenticeships in Science and
Engineering program.

The gene order on these maps is based on recombination in multiple-point
crosses or on duplication-coverage. The order is reliable but relative
distances are often inaccurately determined and are variable in different
genetic backgrounds. The overall length of the maps is estimated using
meiotic recombination frequencies:

Linkage Group

Estimated Size (Mb)

I

10.3

II

4.6

III

5.1

IV

5.7

V

9.2

VI

4.0

VII

4.0

Marker Positions

Positions of markers on the genetic maps are only rough approximations.
Different strains used for mapping exhibit different recombination frequencies
and recombination values for the same interval have been shown to vary
10-fold or more in crosses of different parentage. For this reason, no
attempt has been made to correct for undetected multiple crossovers in
long intervals by using a mapping function.

Distances between markers were estimated as composite or representative
values based on all the crosses available and are shown on the scale where
10 map units = 7% recombination. It must be stressed that absolute and
relative positions on the maps possess only limited predictive value, depending
on the genotype of a particular cross with respect to genes that determine
the frequency of recombination in each local region. In contrast, gene
order is constant in the absence of rearrangement.

Units on the genetic map represent distance from the centromere.

Negative distances denote positions on the left arm

Positive distances denote positions on the right arm

Marker Sequence

296 genetic markers have associated sequence. Most of the available marker
sequence is from Neurospora crassa itself, but in some cases the
sequence is derived from a homologous gene in
Saccharomyces cerevisiae.

Genetic Marker Data

There are 1046 known genetic markers assigned to linkage groups for
Neurospora
crassa. Of these markers:

#

%

Description

457

44%

well-ordered within a genetic map linkage group

296

28%

have associated sequence

111

11%

well-ordered with sequence

Breakpoint Naming

The naming of breakpoints on our maps differs slightly from the names on
the published maps from the Compendium. We have included the linkage group
in the name in some cases to make the name unique in the genome. For example,
the breakpoint T(ALS176) that occurs on linkage groups II and V has been
named T(ALS176)II and T(ALS176)V in our database. In addition, the superscripts
in the breakpoint names, such as T(OY330)L, have been removed
so that the name now looks like T(OY330)I(L).

Correlation to Physical Map

Methodology

All genetic markers with associated sequence were compared to the current
assembly using BLASTN. Where these matches were unique, were of high quality,
and contained most or all of the gene, we assigned a marker position in
one of our contigs. The resulting alignments were used to correlate contigs
with linkage groups:

294 of the 296 markers with sequence (99%) successfully mapped to the current
assembly

66 supercontigs, representing 30.5 Mb (79% of the assembly), are anchored
to a linkage group

We used the subset of sequenced markers that were well ordered on the genetic
maps to order and orient supercontigs:

110 of the 111 well-ordered markers (99%) successfully mapped to current
assembly

46 supercontigs, representing 25.7 Mb (67% of the assembly), are ordered
and oriented on a linkage group map

Special Cases

Markers with sequence, not placed in assemblyIn addition, several markers with sequence have not been assigned a position
in the assembly. This may mean that the marker is not in the current
assembly, or that the BLASTN results did not point to a unique location
in the genome. The following markers have not been assigned a position:

Marker

Linkage Group

nuc-2

II

rg-2

I

Discrepancies

There are a few cases where marker order on the linkage group map conflicts
with the locations of markers in supercontigs. These differences are indicated
visually by crossed lines on the Correspondence of
Physical to Genetic Maps. The discrepancies may be due to:

Errors in assembly of sequence into contigs or supercontigs

Errors in order of markers on the linkage group map

Correct but incomplete assembly data: for example, one supercontig may
lie within a gap between contigs in another supercontig

Map Correlation Data

You can graphically view the correlation between the physical and genetic
linkage maps from the Genetic Maps page.

You can download an XML file listing all markers (including
GI numbers for those with sequence, and contig positions for those located
in our assembly): neurospora_crassa_7_assembly_map.xml
(see Download for data details).